GapMind for catabolism of small carbon sources

 

Alignments for a candidate for epi in Pontibacillus litoralis JSM 072002

Align Methylmalonyl-CoA epimerase; DL-methylmalonyl-CoA racemase; EC 5.1.99.1 (characterized)
to candidate WP_036833956.1 N784_RS07955 methylmalonyl-CoA epimerase

Query= SwissProt::O58010
         (136 letters)



>NCBI__GCF_000775615.1:WP_036833956.1
          Length = 276

 Score =  140 bits (354), Expect = 1e-38
 Identities = 63/129 (48%), Positives = 99/129 (76%), Gaps = 1/129 (0%)

Query: 6   KRIDHVGIAVKNLEEAIKIW-EGLGFKVEEIEEVPDQKVKVAVIKVGENRIELLEATTED 64
           +++ H+GIAV ++E+A+  +   LG ++  +EEV  ++VKVA +++GE +IELLE T ++
Sbjct: 142 EKLAHIGIAVNSIEQALPFYTNALGLRLTGVEEVASEQVKVAFVEIGETQIELLEPTDDN 201

Query: 65  SPIAKFIEKRGEGIHHLAIRVENIESKLEELKQKGYKLIDEKPRVGAGGAKIAFIHPKSV 124
           SPIAKF+EKRGEGIHH+A+ V +IE +L   K+KG  LI + P++GA  +++AF+HPK+ 
Sbjct: 202 SPIAKFMEKRGEGIHHIAVEVTDIEERLRHYKEKGISLIHDTPKLGAHQSQVAFLHPKAT 261

Query: 125 TGVLLELCE 133
            GVL+ELC+
Sbjct: 262 NGVLMELCQ 270


Lambda     K      H
   0.317    0.138    0.389 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 139
Number of extensions: 5
Number of successful extensions: 2
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 136
Length of database: 276
Length adjustment: 20
Effective length of query: 116
Effective length of database: 256
Effective search space:    29696
Effective search space used:    29696
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 44 (21.6 bits)

Align candidate WP_036833956.1 N784_RS07955 (methylmalonyl-CoA epimerase)
to HMM TIGR03081 (mce: methylmalonyl-CoA epimerase (EC 5.1.99.1))

# hmmsearch :: search profile(s) against a sequence database
# HMMER 3.3.1 (Jul 2020); http://hmmer.org/
# Copyright (C) 2020 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query HMM file:                  ../tmp/path.carbon/TIGR03081.hmm
# target sequence database:        /tmp/gapView.1555738.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR03081  [M=129]
Accession:   TIGR03081
Description: metmalonyl_epim: methylmalonyl-CoA epimerase
Scores for complete sequences (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Sequence                             Description
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
    1.3e-51  160.6   1.4      2e-51  160.0   0.6    1.7  2  NCBI__GCF_000775615.1:WP_036833956.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000775615.1:WP_036833956.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0      0.49      0.49      31      54 ..      27      50 ..      24      63 .. 0.63
   2 !  160.0   0.6     2e-51     2e-51       1     129 []     143     270 ..     143     270 .. 0.99

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 0.49
                             TIGR03081 31 eelpeqgvkvvflelgetklelle 54
                                          ++l ++g++v++  l ++  ++++
  NCBI__GCF_000775615.1:WP_036833956.1 27 QALRDHGMEVIYTGLRQSPQQIVQ 50
                                          556777777777777666555554 PP

  == domain 2  score: 160.0 bits;  conditional E-value: 2e-51
                             TIGR03081   1 kldhvaiavkdleeaaklyrdvlGakvseeeelpeqgvkvvflelgetklellepleedspiakflekkkgeG 73 
                                           kl h++iav+++e+a  +y+++lG++++  ee++ ++vkv+f+e+get++ellep++++spiakf+ek+ geG
  NCBI__GCF_000775615.1:WP_036833956.1 143 KLAHIGIAVNSIEQALPFYTNALGLRLTGVEEVASEQVKVAFVEIGETQIELLEPTDDNSPIAKFMEKR-GEG 214
                                           689******************************************************************.*** PP

                             TIGR03081  74 lhhialevddieaaletlkekgvrlldeepriGahGkkvaFlhPkdtgGvLielee 129
                                           +hhia+ev+die+ l++ kekg+ l++++p++Gah  +vaFlhPk t+GvL+el++
  NCBI__GCF_000775615.1:WP_036833956.1 215 IHHIAVEVTDIEERLRHYKEKGISLIHDTPKLGAHQSQVAFLHPKATNGVLMELCQ 270
                                           ******************************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (129 nodes)
Target sequences:                          1  (276 residues searched)
Passed MSV filter:                         1  (1); expected 0.0 (0.02)
Passed bias filter:                        1  (1); expected 0.0 (0.02)
Passed Vit filter:                         1  (1); expected 0.0 (0.001)
Passed Fwd filter:                         1  (1); expected 0.0 (1e-05)
Initial search space (Z):                  1  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 11.59
//
[ok]

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory